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CHAPTER 24 Genes and Chromosomes - Coggle Diagram
CHAPTER 24 Genes and Chromosomes
基本知識
Central Dogma
Information from parental DNA is copied to daughter DNA with high fidelity via DNA replication.
RNA is synthesized using DNA as a template during transcription.
Once information has got into a protein it can’t get out again
Proteins are synthesized based on the information stored in ribonucleotide triplets in RNA during translation
double-helical structure of DNA
DNA&RNA
DNA Is a Very Large Macromolecule
In transcription, one strand of double-stranded DNA acts as the molecular template for RNA synthesis(DNA => messenger RNA).
In translation, the triplets of nucleotides in mRNA bind to complementary triplets in tRNA.
Protein sequence determines its biological function.
How DNA Codes for mRNA That Then Codes for the Amino Acid Sequence
Complexity& Sequences
Some Bacterial Genomes
Also Contain Introns
Until 1993, scientists thought that introns appeared only in eukaryotes.
About 25% of sequenced bacterial genomes show presence of introns.
Introns in bacterial chromosome do not interrupt protein-coding sequences; they interrupt mainly tRNA sequences.
Introns in phage genomes within bacteria interrupt protein-coding sequences.
Many bacterial introns encode catalytic RNA sequences that have the ability to insert and reverse transcribe themselves into the genomic DNA.
Transposons Are Sequences That
Can Move Within the Genome
The eukaryotic genome is not completely static.
Sequences called transposons can move around within the genome of a single cell.
The ends of transposons contain terminal repeats.
These repeats hybridize with complementary regions of target DNA during insertion.
Transposons account for ~50% of the human genome.
Introns in Two Eukaryotic Genes
Eukaryotes Also Contain Highly Repetitive
DNA or Simple Sequence Repeats (SSRs)
Short sequences of ~10 bp or less
Repeated millions of times
Also known as “satellite” DNA
– because when fragmented and centrifuged, the DNA separates into a discrete “satellite” band
Associated with centromeres and telomeres
Eukaryotic Genes Contain
Intervening Sequences (Introns)
Exons are expressed sequences (translated into amino acid sequence).
– Exons account for only 1.5% of human DNA!
Introns are regions of genes that are transcribed but not translated.
– They do not encode polypeptide sequence.
Introns are removed after transcription and the exon mRNA sequences are spliced together.
– creates “mature transcripts”
Telomeres and Centromeres in a Yeast Chromosome
Composition of the Human Genome
Notice that only a small fraction (1.5%) of the total genome encodes for proteins.
The biological significance of noncoding
sequences is not entirely clear.
Some DNA regions directly participate in the regulation of gene expression (promoters, termination signals, etc.).
Some DNA encodes for small regulatory RNA with poorly understood functions.
Some DNA may be junk (pieces of unwanted genes, remnants of viral infections).
Centromere Sequences Are Where
Proteins Attach During Mitosis
Region where the chromatids are held together during mitosis
– that is, after DNA replication but before cell division
Essential for equal distribution of chromosome sets to daughter cells
Have AT-rich repeated sequences of ~130 bp
DNA Is Packaged with Proteins
Viral genomic DNA may be associated with capsid proteins.
Prokaryotic DNA is associated with proteins in the nucleoid.
Eukaryotic DNA is organized with proteins into a complex called chromatin.
Telomere Sequences Cap the Ends of Eukaryotic Chromosomes
DNA, Chromosomes, Genes,
and Complexity
Neither the total length of DNA nor the number of chromosomes correlates strongly with the complexity of an organism .
The correlation between genome size and complexity is poor because most of eukaryotic DNA is noncoding.
Recent experimental work by Craig Venter suggests that a living organism could get by with less than 400 genes.
Telomeres Are Associated with Cellular Aging
In many tissues, telomeres are shortened after each round of replication.
Thus, the cellular DNA “ages.”
Normal human cells divide about 52 times before losing the ability to divide again (Hayflick limit).
Supercoiling
Effects of DNA Underwinding
Linking Number (Lk) Describes Supercoiling
In circular DNA, changing the helical turns requires breaking a strand transiently.
Linking number in relaxed DNA: Lk = #bp / #bp/turn
Lk is an integer for closed-circular DNA and is (+), reflecting a right-handed helix.
Relaxed and Increasingly Supercoiled Plasmid DNA
Lk Is the Number of Times a Strand Penetrates a Surface
Watson-Crick Model of B-DNA
Lk Applied to Closed-Circular DNA
Most Cellular DNA Is Underwound
Normal B-form, relaxed DNA: 10.5 bp/turn (T, twist/turn)
Closed circular DNA is rarely relaxed.
The strain induces supercoiling.
The strain is due to fewer helical turns (underwinding).
Underwinding makes later separation of the strands easier.
Linear DNA is underwound with the help of proteins to prevent strands from rotating.
Changes in Lk Are Useful for Describing Supercoiling
Consider a relaxed DNA of 2100 bp : Lk0 = 200
Underwind by removing two helical turns : Lk = 198 , Δ Lk = 198 – 200 = –2
The Effects of Replication and Transcription on DNA Supercoiling
Superhelical Density, σ
Also known as Specific Linking Difference
Expresses change in Lk in a quantity independent of DNA length
Ratio of # turns removed to Lk,
For most cellular DNAs, σ = -0.05 to -0.07
Closing DNA in a Loop Introduces Supercoiling
Negative and Positive Supercoils
Supercoiling Is the Coiling of a Coil
Nonsupercoiled DNA is called relaxed.
Many circular DNAs are supercoiled.
Supercoiling has great influence on transcription and replication of DNA.
Supercoiling can be highly regulated.
Linking Number Can Be Broken Down
into Twist (Tw) and Writhe (Wr)
Lk = Tw + Wr
Twist (Tw) is the # twists or turns of the helix
Writhe (Wr) is the # coils
typically a negative value
Helical Supercoils
Underwinding Facilitates Additional
DNA Structural Changes
Helps to maintain structure of cruciforms at palindromes(next slide)
Cruciforms rarely occur in relaxed DNA.
Facilitates formation of stretches of left-handed Z form
DNA Supercoiling
DNA in the cell must
be organized to allow:
access of proteins to read the information in DNA sequence
packing of large DNA molecules within the cells
There are several levels of organization, one of which is the supercoiling of the double-stranded DNA helix.
Cruciforms
Size & Amount of DNA
Bacterial Genomes Are Double-Stranded Circles
(Bacteria also contain extra-chromosomal, double-stranded circular plasmids.)
Length of E. Coli DNA Relative to Length of Cell
Many Viral Genomes Are RNA
Many viruses: only RNA or DNA surrounded by protein coat
RNA genomes may be small and single-stranded.
Genomes may change from circular to linear, and so on, during the life cycle.
DNA from Lysed E. Coli Cell Containing Plasmids
How Many Genes per Organism?
E. coli (single circular chromosome) – 4,639,675 bp => ~4300 genes for proteins and ~157genes for catalytic or structural RNAs
Human (24 discrete chromosomes) – 3.1 billion bp => ~20,000 genes
Topoisomers
Eukaryotic Topoisomerases Include
Topo I, IIα, IIβ, IV
Topo I and III are Type I (as in E. coli).
Type II topoisomerases include two subfamilies—Type IIA and Type IIB.
– can relax both positive and negative supercoils
Diversity of DNA Topoisomerases
Type 1 Topoisomerase
Mechanism of a Eukaryotic Type IIα Topoisomerase
The Topoisomerases I–IV of E. Coli
Topo I and III are Type I.
remove negative supercoils to relax DNA
increase Lk
use single-stranded breaks
Topo II is called DNA gyrase.
introduces negative supercoils
decreases Lk
uses ATP and double-stranded breaks
Topoisomerases Are Targets for Antibiotics
Coumarins (novobiocin, coumermycin A1)
inhibit bacterial Type II topoisomerases from binding ATP
Quinolones (nalidixic acid; ciproflaoxadin, Cipro)
inhibit the last step, which is resealing the DNA strand breaks
wide-spectrum and mostly selective for bacterial enzymes
Topoisomerases Are Enzymes
That Change Lk
These enzymes are required for DNA unwinding and rewinding during transcription and replication.
Type I – make a transient cut in one DNA strand, changes Lk by 1
Type II – make a transient cut in both DNA strands, change Lk in steps of 2
Topoisomerase Inhibitors Used as Chemotherapy Agents
Targets cancer because most rapidly growing cells (tumors, others) express topoisomerases
Eukaryotic Type I topoisomerase inhibitors
Eukaryotic Type II topoisomerase inhibitors
Topoisomers in Electrophoresis
Topoisomerase Inhibitors Used as Antibiotics
Topoisomers Are DNAs That
Differ Only in Linking Number
Same # bp, same sequence but different degree of supercoiling
Conversion between topoisomers requires a DNA strand break.
Note that negatively supercoiled DNA (more compact) travels faster in an agarose gel electrophoresis experiment than relaxed or nicked DNA do.
Topoisomerase Inhibitors Used as Chemotherapy Drugs
type
Complete Set of Human Chromosomes (Male)
Mitochondria and Chloroplasts
Also Have DNA
Double-stranded circles
Human mitochondrial DNA (mtDNA)
– 16,569 bp
– ~2–10 copies per mitochondrion
Plant mtDNA
– 200,000–2,500,000 bp
Chloroplast DNA (cpDNA)
– 120,000–160,000 bp
Eukaryotic Chromosome
A pair of linked and condensed sister chromatids of a human chromosome.
Eukaryotic chromosomes are in this state after replication at metaphase during mitosis.
Mitochondrial DNA
It codes for mitochondrial rRNAs, tRNAs, and some of the mitochondrial specific proteins.
Most mitochondrial proteins (at least 95%) are encoded by nuclear genes.
Eukaryote DNA Is in Multiple
Discrete Chromosomes
The number varies with species.
Human somatic (non-sex) cells have 46 chromosomes.
Types of RNA
Structures
Plectonomic and Solenoidal Supercoiling
Eukaryotic Chromosome Structure
Changes over the Course of a Cell Cycle
Nondividing state (G0) and interphase (Gap1, G1; synthesis, S; and Gap2, G2):Chromatin is amorphous and randomly dispersed.
Prophase of mitosis – Chromosomes become condensed, and pairs of sister chromatids form.
Plectonemic Supercoiling
Changes in Chromosome Structure During the Cell Cycle
Supercoiled DNA Forms Plectonemic or Toroid/Solenoid Structures (or a Combination)
Plectonemic
seen in plasmids
involves a right-hand superhelix with terminal loops
Toroid/solenoid
used in chromatin
involves tight left-hand turns
can resemble a garden hose on a reel
provides more compaction
其他
Nucleosomes Consist of DNA
Wrapped Around Histones
DNA of length 105 μm => fits into a nucleus of diameter 5–10 μm.
Partial unfolding reveals “beads on a string.”
Beads are ~146 bp of DNA wrapped around eight histones (the“core”); there are two of each: H2A, H2B, H3, H4.
It forms a left-hand solenoid.
The string is a “linker” DNA of ~54 bp bound to histone H1.
Amino-terminal tails of histones stick out, form sites for covalent modification, and form important contacts between nucleosomes.
DNA Wrapped Around a Histone Core
Nucleosomes
Front and Side Views of Histone Amino- Terminal Tails
DNA Packing into Chromatin
Chromatin consists of fibers of protein and DNA and a small amount of RNA.
DNA associates tightly with proteins called histones.
DNA and protein are packed into discrete units called nucleosomes.
How Amino-Terminal Tails Interact Between Nucleosomes